Summary of Study ST003827
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002390. The data can be accessed directly via it's Project DOI: 10.21228/M8Q250 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003827 |
| Study Title | Polar metabolite profiling of mouse cerebrospinal fluid (CSF) from control mice and mice with leukemia in the central nervous system (CNS) |
| Study Summary | To investigate the effects CNS leukemia on the cerebrospinal fluid metabolome, CSF was collected from control, healthy NOD-SCID mice, and compared to CSF collected from terminal mice that received human leukemia cells into the CNS by intracisternal injection. This study revealed amino acid and nucleoside changes in the CSF. |
| Institute | Boston Childrens Hospital |
| Last Name | Wong |
| First Name | Alan |
| Address | 300 Longwood Avenue |
| alan.wong@childrens.harvard.edu | |
| Phone | (617) 355-7433 |
| Submit Date | 2025-03-26 |
| Num Groups | 4 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-12-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002390 |
| Project DOI: | doi: 10.21228/M8Q250 |
| Project Title: | In vivo CRISPR screen identifies copper metabolism as a vulnerability in acute lymphoblastic leukemia |
| Project Summary: | The nutrient-sparse cerebrospinal fluid (CSF) poses a significant challenge to spreading cancer cells. Despite this challenge, leukemia often spreads to the CSF and represents a significant clinical complication. To uncover nutritional dependencies of leukemia cells in the CSF that could be targeted therapeutically, we conducted an in vivo targeted CRISPR screen in a xenograft model of leukemia. We found that SLC31A1, the primary cell surface copper importer, is a genetic dependency of leukemia in both the central nervous system as well as in the hematopoietic organs. Perturbation of copper metabolism leads to complex IV deficiency, perturbed nucleotide metabolism and slowed leukemia cell proliferation. Furthermore, nutritional copper depletion reduced cancer progression in cell line based and patient-derived xenograft models of leukemia. Copper thus appears to be an actionable micronutrient in leukemia. |
| Institute: | Boston Children's Hospital |
| Department: | Pathology |
| Laboratory: | Naama Kanarek |
| Last Name: | Wong |
| First Name: | Alan |
| Address: | 300 Longwood Avenue, Boston, MA, 02115, USA |
| Email: | alan.wong@childrens.harvard.edu |
| Phone: | (617) 355-7433 |
| Funding Source: | NCI 1R01CA282477-01A1 |
Subject:
| Subject ID: | SU004638 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | NOD-SCID |
| Age Or Age Range: | 8-12 weeks |
| Gender: | Male and female |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Cancer |
|---|---|---|---|
| SA530561 | 20230304_QE1_HILIC_ICcellsandCSF_AYW901 | mouse CSF | CNS_leukemia |
| SA530562 | 20230304_QE1_HILIC_ICcellsandCSF_AYW902 | mouse CSF | CNS_leukemia |
| SA530563 | 20230304_QE1_HILIC_ICcellsandCSF_AYW903 | mouse CSF | CNS_leukemia |
| SA530564 | 20230304_QE1_HILIC_ICcellsandCSF_AYW904 | mouse CSF | CNS_leukemia |
| SA530565 | 20230304_QE1_HILIC_ICcellsandCSF_AYW905 | mouse CSF | CNS_leukemia |
| SA530566 | 20230304_QE1_HILIC_ICcellsandCSF_AYW906 | mouse CSF | control |
| SA530567 | 20230304_QE1_HILIC_ICcellsandCSF_AYW907 | mouse CSF | control |
| SA530568 | 20230304_QE1_HILIC_ICcellsandCSF_AYW908 | mouse CSF | control |
| SA530569 | 20230304_QE1_HILIC_ICcellsandCSF_AYW909 | mouse CSF | control |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO004631 |
| Collection Summary: | Mice were anesthetized using ketamine+xylazine injection and anesthesia verified by toe pinch. Following surgery to open the skin and muscular layers at the posterior aspect of the skull, the area of the skull overlaying the cisterna magna was appreciated. Using a glass microcapillary needle, CSF was withdrawn with gentle suction from the cisterna magna. |
| Sample Type: | Cerebrospinal fluid |
Treatment:
| Treatment ID: | TR004647 |
| Treatment Summary: | 8-12 week old NOD-SCID mice received 50,000 human SEM leukemia cells by intracisternal injection in 10uL of 0.9% NaCl saline. Mice were monitored until terminal disease was reached (approx. 4 weeks), and then CSF was collected from the mice. Healthy, untreated control mice had CSF collected on the same day. |
Sample Preparation:
| Sampleprep ID: | SP004644 |
| Sampleprep Summary: | The CSF was spun at 350g in a 4C centrifuge for 5 minutes. If blood was noted at the bottom of the tube, the sample was discarded. The supernatan CSF was transferred to a new tube. Then, 10uL of CSF from each animal was transferred to a new tube. 160uL of 100% LC-MS grade methanol supplemented with isotopically-labelled amino acid standards [Cambridge Isotope Laboratories, MSK-A2-1.2], aminopterin, and reduced glutathione standard [Cambridge Isotope Laboratories, CNLM-6245-10]). with repeated pipetting up and down and vortexing for 10 seconds. Then, 40uL of LCMS-grade water containing 125 mM Ammonium Acetate, 10 mM Na-Ascorbate, and 7.9 mg/mL 5,5-dithio-bis-(2-nitrobenzoic acid (Ellman's reagent) was added, and the sample vortexex for another 10 seconds. Samples were then centrifuged for 10 minutes at 18,000 g to pellet debris. The supernatant was transferred to a new tube and dried on ice using a liquid nitrogen dryer and stored at -80C. The dried metabolites were then resuspended in 16uL and 2uL was injected. |
Combined analysis:
| Analysis ID | AN007479 |
|---|---|
| Chromatography ID | CH005671 |
| MS ID | MS007175 |
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | Normalized peak area |
Chromatography:
| Chromatography ID: | CH005671 |
| Chromatography Summary: | 2 μL of each sample was injected into a ZIC-pHILIC 150 x 2.1 mm (5 μm particle size) column (EMD Millipore) operated on a Vanquish™ Flex UHPLC system (Thermo Fisher Scientific). Chromatographic separation was achieved using the following conditions: buffer A was acetonitrile; buffer B was 20 mM ammonium carbonate, 0.1% ammonium hydroxide in water; resulting pH is around 9 without pH adjustment. Gradient conditions used were: 0-20 min: linear gradient from 20% to 80% B; 20-24 min: hold at 80% B; 24-24.1 min: from 80% to 20% B; 24.1-32 min: hold at 20% B at 0.150 mL/min flow rate. The column oven and autosampler tray were held at 25 °C and 4 °C, respectively. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Column Temperature: | 25 |
| Flow Gradient: | linear gradient from 20 to 80% B; 20–20.5 min: from 80 to 20% B; 20.5–28 min: hold at 20% B. |
| Flow Rate: | 0.15 mL/min |
| Solvent A: | 100% acetonitrile |
| Solvent B: | 100% water; 20mM ammonium carbonate; 0.1% ammonium hydroxide |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS007175 |
| Analysis ID: | AN007479 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS data acquisition was performed using a QExactive benchtop orbitrap mass spectrometer equipped with an Ion Max source and a HESI II probe (Thermo Fisher Scientific) and polarity switching was used. Four scans were used: full scans in both positive and negative ionization mode in a range of m/z = 70–1000, with the resolution set at 70,000, the AGC target at 1 × 106, and the maximum injection time (Max IT) at 20 msec from 0-20 minutes. A third scan in the negative mode was used with range of m/z = 220-700 from 0-20 minutes and the same resolution, AGC settings with 30ms Max IT. Lastly, a targeted-SIM scan was added with a resolution of 35k, AGC target 1e5, and max IT 20ms, isolation window = 1.0 m/z, with an inclusion m/z of 503.0552 (corresponding to Ellman-derivatized glutathione). Tune file parameters were: spray voltage = 3.5kV, capillary temperature = 320C, S-lens RF = 50, auxillary gas temperature = 350C. |
| Ion Mode: | UNSPECIFIED |
